## ----eval=FALSE--------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install("deltaGseg") ## ----loadingPackage,message=FALSE--------------------------------------------- library(deltaGseg) ## ----------------------------------------------------------------------------- data(deltaGseg) ## ----loading-trajectories,tidy=FALSE,warning=FALSE---------------------------- dir<-system.file("extdata",package="deltaGseg") traj1<-parseTraj(path=dir, files=c("D_GBTOT1","D_GBTOT2","D_GBTOT3")) ## ----test--------------------------------------------------------------------- traj1 ## ----plottraj1,eval=FALSE----------------------------------------------------- # plot(traj1,name='all') ## ----traj1,tidy=TRUE,warning=FALSE-------------------------------------------- traj1.tr<-transformSeries(object=traj1,method='splitting',breakpoints=1) traj1.tr ## ----figure1,warning=FALSE,fig.width=8,eval=FALSE----------------------------- # plot(traj1.tr) ## ----breakpoints,warning=FALSE,tidy=TRUE-------------------------------------- all_breakpoints<-splitTraj(traj1,segsplits=c(5,5,5)) all_breakpoints ## ----plot-breakpoints,warning=FALSE,fig.width=8,eval=FALSE-------------------- # plot(traj1,breakpoints=all_breakpoints) ## ----mybreaks,warning=FALSE,tidy=TRUE,warning=FALSE--------------------------- mybreaks<-chooseBreaks(all_breakpoints,numbreaks=3) mybreaks ## ----transform,warning=FALSE,tidy=TRUE,warning=FALSE-------------------------- traj1.sp.tr<-transformSeries(object=traj1,method='override_splitting',breakpoints=mybreaks) traj1.sp.tr ## ----plot-denoise,warning=FALSE,eval=FALSE,message=FALSE---------------------- # traj1.denoise<-denoiseSegments(object=traj1.tr,seg_method="SegNeigh",maxQ=15,fn=1,factor=0.8,thresh_level=TRUE,minobs=200) ## ----pvals,eval=FALSE--------------------------------------------------------- # pvals<-clusterPV(object=traj1.denoise,bootstrap=500) ## ----clusterPV,warning=FALSE,eval=FALSE,tidy=TRUE----------------------------- # traj1.ss<-clusterSegments(object=traj1.denoise,intervention = "pvclust",pv=pvals) # ##Segment grouping. Click on the root of the groups you want clustered. # ##Please ensure that ALL segments are grouped (boxed). # ##Otherwise, function will not exit. # ##To exit, click Esc (Windows/Linux) or Ctrl-click (Mac) ## ----eval=FALSE--------------------------------------------------------------- # plot(traj1.ss) ## ----getIntervals------------------------------------------------------------- getIntervals(traj1.ss) ## ----warning=FALSE,tidy=TRUE,eval=FALSE--------------------------------------- # diagnosticPlots(object=traj1.ss,norm.test="KS",single.series=TRUE) ## ----------------------------------------------------------------------------- x<-getTraj(traj1.tr)[['D_GBTOT3_1']] y<-x[,2]-35; y1<-y[1:2000]; y2<-y[2001:length(y)]+17 ss<-c(seq(50,length(y2),100),length(y2)) for(i in 1:(length(ss)-1)) y2[ss[i]:ss[(i+1)]]<-y2[ss[i]:ss[(i+1)]]+i^1.85 y<-cbind(x[,1],c(y1,y2)) simtraj<-parseTraj(files=list(y),fromfile=FALSE) simtraj ## ----eval=FALSE--------------------------------------------------------------- # plot(simtraj) ## ----tidy=TRUE,warning=FALSE-------------------------------------------------- simtraj.tr<-transformSeries(object=simtraj,method='splitting',breakpoints=1) simtraj.tr ## ----eval=FALSE--------------------------------------------------------------- # plot(simtraj.tr) ## ----tidy=TRUE,warning=FALSE,eval=FALSE--------------------------------------- # simtraj.tr2<-transformSeries(object=simtraj.tr,method='differentiation') # simtraj.tr2 ## ----eval=FALSE--------------------------------------------------------------- # plotDiff(simtraj.tr2,name="1_2") ## ----------------------------------------------------------------------------- sessionInfo()